Ensembl Compara (e56)

Description

Modified version of the vanilla pipeline to build trees with protein sequences only (no nucleotide sequence, no chromosome coordinates). Please be aware that the Xenopus tropicalis genes homologies are mostly wrong due to an error in the species tree used in the pipeline

OMA GETHOGs 2.0

Description

Hierarchical Orthologous Groups based on pairwise orthologs infered by OMA. The ideas and methodology are described in here, where as this version 2.0 makes use of the new bottom-up algorithm described in here.

OMA Groups (RefSet5)

Description

OMA Groups consists of groups of genes in which all pairs are orthologs. In a graph representation with genes as nodes and orthology relations as edge, OMA groups correspond to fully connected subgraphs. Due to this definition, each OMA group includes at most one sequence per species. The primary intended application of these groups is to provide input data for phylogenetic inference.The inference was done on the reference proteomes with the standard parameters.

OMA Groups 2.0

Description

OMA Groups consists of groups of genes in which all pairs are orthologs. In a graph representation with genes as nodes and orthology relations as edge, OMA groups correspond to fully connected subgraphs. Due to this definition, each OMA group includes at most one sequence per species. The primary intended application of these groups is to provide input data for phylogenetic inference.In this instance of OMA Groups, the pairwise orthologs are based on the relations obtained with the refinements described in OMA 2.0. Additionally, the quasi-cliques that are compatible (no overlapping species) and where at least 50% of the maximal possible edges among the clusters are present, have been merged.

OMA Pairs (Refset5)

Description

The OMA Pairs are the primary product of the OMA pipeline. It is a list of high-confidence pairs of orthologous genes.OMA is based on an algorithm that compares genes on the basis of evolutionary distances, considers distance inference uncertainty, and accounts for differential gene losses.

OMA Pairs 2.0

Description

The OMA Pairs are the primary product of the OMA pipeline. It is a list of high-confidence pairs of orthologous genes.OMA is based on an algorithm that compares genes on the basis of evolutionary distances, considers distance inference uncertainty, and accounts for differential gene losses.The version 2.0 has better support for fast evolving inparalogs. The changes are described in here.

orthoinspector 1.30 (blast threshold 10-9)

Description

OrthoInspectoris a software system for orthology/paralogy analysis. It uses an original algorithm based on pairwise inparalog group comparison to detect one-to-one, one-to-many and many-to-many orthologous relations. It is made available as an independent software suite facilitating the installation and the maintenance of a database and providing several visualization tools for a comprehensive orthology analysis.

PANTHER 8.0 (LDO only)

phylomeDB

Description

PhylomeDB is a public database for complete collections of gene phylogenies (phylomes). Here, we reconstructed 31 phylomes (102-115; 125-133, 205, 206, 210, 219-223) for all 66 species or their subset using various model species as starting point (seed species). In total, 314,086 maximum likelihood trees have been reconstructed, from which 5,567,251 orthologs have been retrieved using Consistency score cut-off of 0.6.

RSD 0.8 1e-5 Deluca

Description

Roundup is a large-scale orthology database. The orthologs are computed using the Reciprocal Smallest Distance (RSD) algorithm. This dataset is computed using a divergence parameter of 0.8 and an E-value cutoff of 1e-5.